RetrogeneDB ID: retro_atau_10

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold85694:5788..6994(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: F775_01905
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_31516
• Aliases: None
• Description: None

Sequence

>retro_atau_10
ATGATGAACCCGGAGATGATGCGGGTGGCGGAGGAGCAGATGCGACGCATCCCCGCCGTCGACCTCGCCAGGATGCAGCG
GCAGCTCATGTCCAACCCGGACCTGCTAAAGCTCACAACCGAGAGCATGAAGAACATGACGGCCGAGGACTTCAAGCTCG
CCGCCGAGTGCCTGAACCACGCAAGGCCAGAGGAGATGCTCGACATGACCGAGAAAATCGCCAAGGCCAAGCCCGAGGAG
CTCGCCGCCATGAAGGCGCAAGCCGACGCTGAGACGTCGCGCGCGATATCCGCCGCCAAGATGCTGAAGCGGCAGGGGAA
CCAGCTCCATGGCCGCGGGCAGTACGCTGACGCCGCCGCCAAGTACAAGCTCGCCAGGGACAGCGTGAAGAACGGCGTGC
CATCGGCGGCTGGGCGCGCTCTGCAGCTGCAGTGCAGCGTTAATCTGATGGCTTGTTACCTGAAATTAGGCGAGTTTGAG
GAGTGCGTCAATGAAGGTTCAGAGGTTTTAAGCTATGAATCGGGCGATGCCAAAGCATACTACCGAAGAGGGCAAGCGTA
CAAACAGCTAGGAAACCTTCATGCTGCTGTTGCTGACTTGAGTAAAGCCCGTGAGATTTCTCCGGACGATGAAACTGTCG
CTCAAGCTCTGGCAGAGGCACAAGAAAAATGTGCGACCGAAGGGGGGACAAAAAACCTGCCAAAGGGAGTTGTCATTGAA
GAAATTGTAGAAGATATTAGTTATGATCTGGCAAGCCCTGAAAACAGTTCTTCTACTACTACTGAGCATACTGCTTCACA
ACCACACGACGGAGCACGAAACTCGACACAATCTGACTCTTCAGAAAGCTTGGTAAATATGTCTCAGGTTGCTTCTTCAT
CAAGTGGAACAATCCCTGTTAGCCCTGCTATGTGGGAGATGTTTGCATCCATGGTGGAGAACATGAGCCCTGATGAAATG
GCAAACATGAGCGGGCTGCTCGGTATCGAGATGTCCAAGGAGGATGCTGCCAACGCTCAACATGCTATGTCTTCATTCTC
TTCACAAGATTTAGAGAAAATGATGAAGTGGATCGGCAGAGCACAGCGAGGAGTCGCAGCGGCAAAGAAGACGAAGGACT
GGCTCCTAGGCAGGAAAGGCTTCATCTTTGCTATTGTCATGCTGATCTTGGCGTTCATCCTCCATCGGCTTGGATTCATC
GGGTAG

Alignment

ORF - retro_atau_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.33 %
• Parental protein coverage: 50.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMDPEMMRLAQEQMRRMSPDDLARMQQQLMSNPDLIKLASESMKNMRTEDFKRAAQQLNQTRPEEMLDMT
          MM.PEMMR.A.EQMRR....DLARMQ.QLMSNPDL.KL..ESMKNM..EDFK.AA..LN..RPEEMLDMT
Retrocopy MMNPEMMRVAEEQMRRIPAVDLARMQRQLMSNPDLLKLTTESMKNMTAEDFKLAAECLNHARPEEMLDMT

Parental  EKIANAKPEEFAAMKAQADAQISYALSGAKMLKQQGNELHSHGKYTDAAAKYKLAKENMKS-IPSAAGRT
          EKIA.AKPEE.AAMKAQADA..S.A.S.AKMLK.QGN.LH..G.Y.DAAAKYKLA....K...PSAAGR.
Retrocopy EKIAKAKPEELAAMKAQADAETSRAISAAKMLKRQGNQLHGRGQYADAAAKYKLARDSVKNGVPSAAGRA

Parental  LQLQCTLNLMSCYLKSGMFDECVNEGSEVLTYDSSNVKAYYRRGQAYKELGNLQAAVADLRKAHEISPED
          LQLQC..NLM.CYLK.G.F.ECVNEGSEVL.Y.S...KAYYRRGQAYK.LGNL.AAVADL.KA.EISP.D
Retrocopy LQLQCSVNLMACYLKLGEFEECVNEGSEVLSYESGDAKAYYRRGQAYKQLGNLHAAVADLSKAREISPDD

Parental  ETIAEVLRDTDAKLATEGGGTNLPKGVVIEEIVEEDSSELLSTQRSSS--TEYTVSQPHEGAGNSRQSDS
          ET.A..L.....K.ATEGG..NLPKGVVIEEIVE..S..L.S...SSS..TE.T.SQPH.GA.NS.QSDS
Retrocopy ETVAQALAEAQEKCATEGGTKNLPKGVVIEEIVEDISYDLASPENSSSTTTEHTASQPHDGARNSTQSDS

Parental  SESLMN
          SESL.N
Retrocopy SESLVN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Aegilops tauschii was not studied using RNA-Seq expression data.

ChIP-Seq

Aegilops tauschii was not studied using ChIP-Seq data.

EST

Aegilops tauschii was not studied using EST data.

TSS

Aegilops tauschii was not studied using FANTOM5 data.

Lab

retro_atau_10 was not experimentally validated.

Homology

Retrocopy orthology:

Aegilops tauschii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI1G56980	1 retrocopy	retro_bdis_36,
Aegilops tauschii	F775_31516	1 retrocopy	retro_atau_10 ,
Hordeum vulgare	MLOC_56431	1 retrocopy	retro_hvul_94,
Oryza barthii	OBART07G03860	1 retrocopy	retro_obar_28,
Oryza glaberrima	ORGLA07G0032400	1 retrocopy	retro_ogla_27,